Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold796
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61010
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Found at i:3369 original size:11 final size:11
Alignment explanation
Indices: 3353--3377 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3343 ATTCCCAAAC
3353 TTTTTTTCTTT
1 TTTTTTTCTTT
3364 TTTTTTTCTTT
1 TTTTTTTCTTT
3375 TTT
1 TTT
3378 GGTAAATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:4842 original size:40 final size:41
Alignment explanation
Indices: 4749--4852 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 41
4739 TATTAAATAT
4749 ATTTATTTAAATTTAATT-TGATTTAAAATATAAATATTAAA
1 ATTTATTTAAATTTAATTAT-ATTTAAAATATAAATATTAAA
* * *
4790 TTTTATTTAAATTTAGTTATATTTATAA-AT-AATAATTAAA
1 ATTTATTTAAATTTAATTATATTTAAAATATAAAT-ATTAAA
* *
4830 ATTTATTAAAATTTATTTATATT
1 ATTTATTTAAATTTAATTATATT
4853 ATATTTTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
39 3 0.05
40 28 0.51
41 23 0.42
42 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (41 bp):
ATTTATTTAAATTTAATTATATTTAAAATATAAATATTAAA
Found at i:4862 original size:14 final size:14
Alignment explanation
Indices: 4840--4891 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
4830 ATTTATTAAA
4840 ATTTATTTATATTAT
1 ATTT-TTTATATTAT
4855 ATTTTTTATAATT-T
1 ATTTTTTAT-ATTAT
* *
4869 ATTTTTTAAAATAT
1 ATTTTTTATATTAT
*
4883 AATTTTTAT
1 ATTTTTTAT
4892 TAATTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 2 0.06
14 22 0.71
15 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTTTATATTAT
Found at i:6100 original size:18 final size:19
Alignment explanation
Indices: 6065--6106 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
6055 GCAAAAATTG
*
6065 TATAAAATTAGTTTTGTTA
1 TATAAAATTAGATTTGTTA
6084 TATAAAATTA-ATTTGTTA
1 TATAAAATTAGATTTGTTA
*
6102 AATAA
1 TATAA
6107 TTGAATATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
TATAAAATTAGATTTGTTA
Found at i:6394 original size:3 final size:3
Alignment explanation
Indices: 6388--6417 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6378 TTAATTATTA
6388 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6418 CAATGGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6649 original size:16 final size:16
Alignment explanation
Indices: 6630--6673 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
6620 ATCTTGAATC
* *
6630 ATTTTAATTTTAAATT
1 ATTTTAAATTAAAATT
6646 ATTTTAAATTAAAATT
1 ATTTTAAATTAAAATT
* *
6662 AATTAAAATTAA
1 ATTTTAAATTAA
6674 TTTTTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAATTAAAATT
Found at i:9284 original size:7 final size:7
Alignment explanation
Indices: 9260--9305 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
9250 TTCAAATCAA
*
9260 TTAAAAT
1 TTAAATT
9267 TTAAATTTT
1 TTAAA--TT
*
9276 TTTAATT
1 TTAAATT
9283 TTAAATT
1 TTAAATT
9290 TTAAATT
1 TTAAATT
9297 TTAAATT
1 TTAAATT
9304 TT
1 TT
9306 TTTAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 29 0.85
9 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTAAATT
Found at i:9314 original size:14 final size:15
Alignment explanation
Indices: 9264--9316 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 15
9254 AATCAATTAA
9264 AATTTAAATTTTTTT
1 AATTTAAATTTTTTT
*
9279 AATTTTAAA--TTTTA
1 AA-TTTAAATTTTTTT
9293 AATTTTAAATTTTTTT
1 AA-TTTAAATTTTTTT
9309 AA-TTAAAT
1 AATTTAAAT
9317 CAAAATCTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 19 0.58
15 2 0.06
16 12 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTAAATTTTTTT
Found at i:11006 original size:16 final size:16
Alignment explanation
Indices: 10984--11037 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
10974 TATAATCAAG
10984 TTATTTTGTATTTAAA
1 TTATTTTGTATTTAAA
*
11000 ATATTTT-TATTTTAAA
1 TTATTTTGTA-TTTAAA
*
11016 TTATTTTGAATTTAAA
1 TTATTTTGTATTTAAA
11032 TTATTT
1 TTATTT
11038 CGAGCTCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 30 0.91
17 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
TTATTTTGTATTTAAA
Found at i:12616 original size:18 final size:18
Alignment explanation
Indices: 12593--12629 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12583 AAGATAATAA
12593 TATTAATCTTTTATTTAT
1 TATTAATCTTTTATTTAT
12611 TATTAATCTTTTATTTAT
1 TATTAATCTTTTATTTAT
12629 T
1 T
12630 TATCTGTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTAATCTTTTATTTAT
Found at i:15621 original size:36 final size:35
Alignment explanation
Indices: 15575--15685 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 35
15565 TTAAAAAGAT
*
15575 AAAAAA-CTTAAAGTGCTTTAAATACATTATTTTAA
1 AAAAAATCTTAAAGTACTTTAAATACATTA-TTTAA
* * *
15610 AAAAAATCTTAAAGCACTTTTAATATATTATTTAA
1 AAAAAATCTTAAAGTACTTTAAATACATTATTTAA
* *
15645 AGAAAAGATCCTAAAGTACTTTAAGTACATTATTTAA
1 A-AAAA-ATCTTAAAGTACTTTAAATACATTATTTAA
15682 AAAA
1 AAAA
15686 TAAAAGAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
35 12 0.19
36 26 0.41
37 26 0.41
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (35 bp):
AAAAAATCTTAAAGTACTTTAAATACATTATTTAA
Found at i:17767 original size:16 final size:15
Alignment explanation
Indices: 17748--17836 Score: 72
Period size: 16 Copynumber: 5.7 Consensus size: 15
17738 ATTAAGTATG
17748 AATTATTTTGAATTTA
1 AATTATTTT-AATTTA
*
17764 AATTATTTTCGATTTA
1 AATTATTTT-AATTTA
*
17780 AA-TCTTTTAAGTTTA
1 AATTATTTTAA-TTTA
* *
17795 AGTCATTTTAAGTTTA
1 AATTATTTTAA-TTTA
* *
17811 AAGTCTTTTAAATTTA
1 AATTATTTT-AATTTA
17827 AATTATTTTA
1 AATTATTTTA
17837 GATTCGGGCT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
14 1 0.02
15 11 0.19
16 43 0.75
17 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (15 bp):
AATTATTTTAATTTA
Found at i:17827 original size:32 final size:31
Alignment explanation
Indices: 17753--17836 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
17743 GTATGAATTA
* * *
17753 TTTTGAATTTAAATTATTTT-CGATTTAAATC
1 TTTTAAATTTAAATCATTTTAAG-TTTAAATC
* *
17784 TTTTAAGTTTAAGTCATTTTAAGTTTAAAGTC
1 TTTTAAATTTAAATCATTTTAAGTTTAAA-TC
*
17816 TTTTAAATTTAAATTATTTTA
1 TTTTAAATTTAAATCATTTTA
17837 GATTCGGGCT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
31 22 0.51
32 21 0.49
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (31 bp):
TTTTAAATTTAAATCATTTTAAGTTTAAATC
Found at i:18290 original size:7 final size:7
Alignment explanation
Indices: 18278--18327 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
18268 GTAAAATTAT
18278 TATTTTA
1 TATTTTA
18285 TATTTTA
1 TATTTTA
**
18292 TAAAATTA
1 T-ATTTTA
18300 TTATTTTA
1 -TATTTTA
18308 TATTTTA
1 TATTTTA
*
18315 TATGTTA
1 TATTTTA
18322 TATTTT
1 TATTTT
18328 TAGTTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 26 0.74
8 8 0.23
9 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (7 bp):
TATTTTA
Found at i:18295 original size:23 final size:23
Alignment explanation
Indices: 18269--18316 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
18259 TTACCGAAGG
18269 TAAAATTATTATTTTATATTTTA
1 TAAAATTATTATTTTATATTTTA
18292 TAAAATTATTATTTTATATTTTA
1 TAAAATTATTATTTTATATTTTA
18315 TA
1 TA
18317 TGTTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAAAATTATTATTTTATATTTTA
Found at i:18908 original size:56 final size:56
Alignment explanation
Indices: 18822--18928 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 56
18812 CTTTATTTCC
*
18822 AAATTTTATTTTTATTACAAAATGGGAATTTTAATCGAAAGAAAAAGTTATGAAAT
1 AAATTTTATTTTTATTACAAAATGAGAATTTTAATCGAAAGAAAAAGTTATGAAAT
* * *
18878 AAATTTTATTTTTATTATAAAATGAGAATTTTAGTCGAAAGGAAAAGTTAT
1 AAATTTTATTTTTATTACAAAATGAGAATTTTAATCGAAAGAAAAAGTTAT
18929 TATTTTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (56 bp):
AAATTTTATTTTTATTACAAAATGAGAATTTTAATCGAAAGAAAAAGTTATGAAAT
Found at i:22078 original size:16 final size:15
Alignment explanation
Indices: 22052--22082 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
22042 ATAAAAAAGA
22052 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
22067 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
22083 TTATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:23452 original size:5 final size:5
Alignment explanation
Indices: 23444--23497 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
23434 GCATGAAAGC
* * * *
23444 AATGC AATGA AATGC AATGA AATGA AATGA AATGA AATGC AATGC AATGA
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA
23494 AATG
1 AATG
23498 TTTTTGAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.20
Consensus pattern (5 bp):
AATGA
Found at i:23459 original size:10 final size:10
Alignment explanation
Indices: 23444--23497 Score: 81
Period size: 10 Copynumber: 5.4 Consensus size: 10
23434 GCATGAAAGC
23444 AATGCAATGA
1 AATGCAATGA
23454 AATGCAATGA
1 AATGCAATGA
*
23464 AATGAAATGA
1 AATGCAATGA
* *
23474 AATGAAATGC
1 AATGCAATGA
23484 AATGCAATGA
1 AATGCAATGA
23494 AATG
1 AATG
23498 TTTTTGAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.20
Consensus pattern (10 bp):
AATGCAATGA
Found at i:23462 original size:15 final size:15
Alignment explanation
Indices: 23436--23497 Score: 90
Period size: 15 Copynumber: 4.2 Consensus size: 15
23426 CATTTCATGC
*
23436 ATGAAA-GCAATGCA
1 ATGAAATGCAATGAA
23450 ATGAAATGCAATGAA
1 ATGAAATGCAATGAA
*
23465 ATGAAATGAAATGAA
1 ATGAAATGCAATGAA
*
23480 ATGCAATGCAATGAA
1 ATGAAATGCAATGAA
23495 ATG
1 ATG
23498 TTTTTGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
14 6 0.14
15 37 0.86
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.19
Consensus pattern (15 bp):
ATGAAATGCAATGAA
Found at i:23571 original size:15 final size:16
Alignment explanation
Indices: 23547--23581 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
23537 ATGTTACGTG
23547 AAAA-GCATGAAAT-A
1 AAAATGCATGAAATGA
23561 AAAATGCATGAAATGA
1 AAAATGCATGAAATGA
23577 AAAAT
1 AAAAT
23582 ATGTGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 9 0.47
16 6 0.32
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (16 bp):
AAAATGCATGAAATGA
Found at i:26315 original size:21 final size:21
Alignment explanation
Indices: 26291--26354 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
26281 TATTTACATT
26291 TTGTTTTCTAAATAATGTACA
1 TTGTTTTCTAAATAATGTACA
* * * * **
26312 TTG-TATAT-ATTAATATATT
1 TTGTTTTCTAAATAATGTACA
*
26331 TTGTTTGCTAAATAATGTACA
1 TTGTTTTCTAAATAATGTACA
26352 TTG
1 TTG
26355 CATAGACTAT
Statistics
Matches: 28, Mismatches: 13, Indels: 4
0.62 0.29 0.09
Matches are distributed among these distances:
19 10 0.36
20 5 0.18
21 13 0.46
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (21 bp):
TTGTTTTCTAAATAATGTACA
Found at i:31926 original size:18 final size:18
Alignment explanation
Indices: 31903--31947 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
31893 TAACACAATA
31903 ATTATATAAAATTAATTT
1 ATTATATAAAATTAATTT
31921 ATTATATAAAATTAATTT
1 ATTATATAAAATTAATTT
*
31939 ATTAAATAA
1 ATTATATAA
31948 TTAAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATATAAAATTAATTT
Found at i:32548 original size:20 final size:20
Alignment explanation
Indices: 32511--32547 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
32501 ATTTAAAAAT
32511 TTTTAAATCACATTTTTTAC
1 TTTTAAATCACATTTTTTAC
32531 TTTTAAA-CACATTTTTT
1 TTTTAAATCACATTTTTT
32548 TCAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAATCACATTTTTTAC
Found at i:33437 original size:68 final size:68
Alignment explanation
Indices: 33328--33465 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 68
33318 GGTAATCAGT
33328 GGCAGAACCGAAAAGGCACCAAATAATGAAATTGCTAAGGTCATTTTATGAAGCGCTAAAAAATC
1 GGCAGAACCGAAAAGGCACCAAATAATGAAATTGCTAAGGTCATTTTATGAAGCGCTAAAAAATC
33393 GGA
66 GGA
* * * *
33396 GGCAGAATCGGAAAGGCACCAAATGATGAAATTGCTAAGGTCATTTTATGAAGCGCTACAAAATC
1 GGCAGAACCGAAAAGGCACCAAATAATGAAATTGCTAAGGTCATTTTATGAAGCGCTAAAAAATC
33461 GGA
66 GGA
33464 GG
1 GG
33466 AATTGGCATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.20
Consensus pattern (68 bp):
GGCAGAACCGAAAAGGCACCAAATAATGAAATTGCTAAGGTCATTTTATGAAGCGCTAAAAAATC
GGA
Found at i:33548 original size:18 final size:18
Alignment explanation
Indices: 33525--33560 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
33515 ATAGTCTTTG
33525 TTATTTT-ATTTCTCCATT
1 TTATTTTAATTT-TCCATT
33543 TTATTTTAATTTTCCATT
1 TTATTTTAATTTTCCATT
33561 AATTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTTAATTTTCCATT
Found at i:34361 original size:16 final size:16
Alignment explanation
Indices: 34331--34375 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
34321 ATTCTTTTGC
* *
34331 ATTTAAAATACTTTA-
1 ATTTAAATTATTTTAG
34346 ATCTTAAATTATTTTAG
1 AT-TTAAATTATTTTAG
34363 ATTTAAATTATTT
1 ATTTAAATTATTT
34376 CAAATTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTAAATTATTTTAG
Found at i:37035 original size:12 final size:12
Alignment explanation
Indices: 37018--37042 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37008 ATTCCCAAAC
37018 TTTTTTCTTTTT
1 TTTTTTCTTTTT
37030 TTTTTTCTTTTT
1 TTTTTTCTTTTT
37042 T
1 T
37043 GGTAAATGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:38440 original size:15 final size:15
Alignment explanation
Indices: 38422--38454 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
38412 ATATTTATAG
38422 ATTAA-ATTAAATAAT
1 ATTAACATTAAAT-AT
38437 ATTAACATTAAATAT
1 ATTAACATTAAATAT
38452 ATT
1 ATT
38455 TATTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAACATTAAATAT
Found at i:38448 original size:21 final size:22
Alignment explanation
Indices: 38405--38449 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
38395 AGATTTTTTC
*
38405 ATTAAAAATATTTATAGATTAA
1 ATTAAAAATATTTATACATTAA
38427 ATTAAATAATA-TTA-ACATTAA
1 ATTAAA-AATATTTATACATTAA
38448 AT
1 AT
38450 ATATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 9 0.43
23 4 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTAAAAATATTTATACATTAA
Found at i:38504 original size:24 final size:23
Alignment explanation
Indices: 38459--38508 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 23
38449 TATATTTATT
38459 TAAATTTAATTTAATTTAAAATA
1 TAAATTTAATTTAATTTAAAATA
*
38482 TAAATTTTAAATTTTATTTAAATATA
1 TAAA-TTT-AATTTAATTTAAA-ATA
38508 T
1 T
38509 TCGTATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 3 0.13
25 12 0.52
26 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTTAATTTAATTTAAAATA
Found at i:38565 original size:14 final size:14
Alignment explanation
Indices: 38548--38609 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
38538 CTTAGACTCA
38548 TTTAT-ATTATATTT
1 TTTATAATT-TATTT
38562 TTTATAATTTATTT
1 TTTATAATTTATTT
* * * *
38576 TTTAAAATGTAATC
1 TTTATAATTTATTT
*
38590 TTTATTAATTTAATT
1 TTTA-TAATTTATTT
38605 TTTAT
1 TTTAT
38610 TATGTTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 25 0.64
15 14 0.36
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTATAATTTATTT
Found at i:38611 original size:15 final size:14
Alignment explanation
Indices: 38560--38609 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
38550 TATATTATAT
*
38560 TTTTTATAATTTAT
1 TTTTTATAATTTAA
* *
38574 TTTTTAAAATGTAA
1 TTTTTATAATTTAA
*
38588 TCTTTATTAATTTAA
1 TTTTTA-TAATTTAA
38603 TTTTTAT
1 TTTTTAT
38610 TATGTTTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (14 bp):
TTTTTATAATTTAA
Found at i:38858 original size:14 final size:13
Alignment explanation
Indices: 38838--38867 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38828 TTTAACATTT
*
38838 TAATTTTTCATAG
1 TAATTTTTTATAG
38851 TAATTTTTTATAG
1 TAATTTTTTATAG
38864 TAAT
1 TAAT
38868 ACTAAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (13 bp):
TAATTTTTTATAG
Found at i:39672 original size:18 final size:18
Alignment explanation
Indices: 39651--39688 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39641 TGTTTTATAC
*
39651 TTTT-TTTTTATTTCTCCA
1 TTTTATTTTAATTT-TCCA
39669 TTTTATTTTAATTTTCCA
1 TTTTATTTTAATTTTCCA
39687 TT
1 TT
39689 AATTGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTTAATTTTCCA
Found at i:39699 original size:79 final size:78
Alignment explanation
Indices: 39572--39748 Score: 327
Period size: 79 Copynumber: 2.3 Consensus size: 78
39562 AAATTATAGT
*
39572 CTTTTTTTTATTTCTCCATTTTATTTTAATTTTCCATTAATTGGTTTTCTAATTTTATGTCCATT
1 CTTTTTTTTATTTCTCCATTTTATTTTAATTTTCCATTAATTGGTTTTCTAATTTTATCTCCATT
39637 TTGTTGTTTTATA
66 TTGTTGTTTTATA
*
39650 CTTTTTTTTTATTTCTCCATTTTATTTTAATTTTCCATTAATTGTTTTTCTAATTTTATCTCCAT
1 C-TTTTTTTTATTTCTCCATTTTATTTTAATTTTCCATTAATTGGTTTTCTAATTTTATCTCCAT
39715 TTTGTTGTTTTATA
65 TTTGTTGTTTTATA
39729 CTTTTTTTTATTTCTCCATT
1 CTTTTTTTTATTTCTCCATT
39749 ATACTATTGT
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
78 20 0.21
79 76 0.79
ACGTcount: A:0.17, C:0.13, G:0.05, T:0.66
Consensus pattern (78 bp):
CTTTTTTTTATTTCTCCATTTTATTTTAATTTTCCATTAATTGGTTTTCTAATTTTATCTCCATT
TTGTTGTTTTATA
Found at i:39974 original size:18 final size:18
Alignment explanation
Indices: 39938--39982 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
39928 TAACACAAAA
* *
39938 GTTATATAAAATTAGTTT
1 GTTATATAAAATCAATTT
*
39956 GTTATATAACATCAATTT
1 GTTATATAAAATCAATTT
*
39974 GTTAAATAA
1 GTTATATAA
39983 TTGAATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (18 bp):
GTTATATAAAATCAATTT
Found at i:40364 original size:17 final size:18
Alignment explanation
Indices: 40333--40370 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40323 TTTTATTAAA
40333 AAAATAAAAAAGAT-ATT
1 AAAATAAAAAAGATAATT
**
40350 AAAATAAAATTGATAATT
1 AAAATAAAAAAGATAATT
40368 AAA
1 AAA
40371 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAATAAAAAAGATAATT
Found at i:40470 original size:16 final size:16
Alignment explanation
Indices: 40451--40516 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
40441 TTATTATAAG
40451 TTTACGATTAAATTAT
1 TTTACGATTAAATTAT
*
40467 TTTACGTTTAAGA-TAT
1 TTTACGATTAA-ATTAT
***
40483 TTTAATTTTAAATTAT
1 TTTACGATTAAATTAT
*
40499 TTTA-AATTTAAATTAT
1 TTTACGA-TTAAATTAT
40515 TT
1 TT
40517 CGAATTCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
15 1 0.02
16 40 0.95
17 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTACGATTAAATTAT
Found at i:40522 original size:16 final size:16
Alignment explanation
Indices: 40458--40527 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
40448 AAGTTTACGA
* **
40458 TTAAATTATTTTACGT
1 TTAAATTATTTCAAAT
* *
40474 TTAAGA-TATTTTAATT
1 TTAA-ATTATTTCAAAT
*
40490 TTAAATTATTTTAAAT
1 TTAAATTATTTCAAAT
*
40506 TTAAATTATTTCGAAT
1 TTAAATTATTTCAAAT
*
40522 TCAAAT
1 TTAAAT
40528 CAATTTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 1 0.02
16 44 0.96
17 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (16 bp):
TTAAATTATTTCAAAT
Found at i:44597 original size:14 final size:14
Alignment explanation
Indices: 44575--44620 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
44565 TTGATATATT
44575 TAATTATTTAATAA
1 TAATTATTTAATAA
**
44589 TTTTTATTTAAATAA
1 TAATTATTT-AATAA
*
44604 TAATTATTAAATAA
1 TAATTATTTAATAA
44618 TAA
1 TAA
44621 CAATCAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATTTAATAA
Found at i:44901 original size:26 final size:25
Alignment explanation
Indices: 44852--44901 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
44842 TTAATTGAAA
* * *
44852 TTTAATTTTTTTTTAGATTTAAATT
1 TTTAATTTTTTATTAAATTAAAATT
44877 TTTAATTTTTTAATTAAATTAAAAT
1 TTTAATTTTTT-ATTAAATTAAAAT
44902 CTAACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTAATTTTTTATTAAATTAAAATT
Found at i:45505 original size:231 final size:229
Alignment explanation
Indices: 45012--45716 Score: 778
Period size: 235 Copynumber: 3.0 Consensus size: 229
45002 CCAATTGGCC
* * ** * * *
45012 AATGGGATGAGGCAAATAAAGATAAATTTGAACACAACATTATCTATTATTTGTATTACTGAAAA
1 AATGAGATGAGGCCAAT-AAGATAAATTTGAAGGCAACATTATCTATCATTTGTATTGCTGAGAA
* * * * * *
45077 AATATGAGAAAGTAGCTGAAAAAAAAAGAAGAGAGAGAAGATATTGATATATTGCTAGTAATTAT
65 AATATGAGAAAGCAGCTGAAAAAAAAAGAAGAGAAAG-AGAAACTGACATATTGCTAGTAATTAG
* * *
45142 ATTATTAATATAAGAAAAATCCAATTAAAATTACAGAAATAGCTCGAGCTTTTCTCAA-TAATAA
129 ATTATTAATATGAGAAAAAT-CAACTAAAATGA-AGAAATAGCTCGAGCTTTTCTCAACT-AT-A
*
45206 TAAAAAAAATTAAGACTTGACATAAACGACTCAATATTA-A
190 -AAAAAAAATTAAGACTTGACATAAATGACTCAATATTATA
* * * * *
45246 CCAATGAGATGAGGCCAATAAAATAAATTTGAGGGTAACCTTATCTATCATTTGTATTGCTGTGA
1 --AATGAGATGAGGCCAATAAGATAAATTTGAAGGCAACATTATCTATCATTTGTATTGCTGAGA
*
45311 AAATATGAGAAAGCAGCTTAAAAAAAAAGAA-AGAAAGAGAAACTGACATATTGCTAGTAATTAG
64 AAATATGAGAAAGCAGCTGAAAAAAAAAGAAGAGAAAGAGAAACTGACATATTGCTAGTAATTAG
* *
45375 ATTATTAGTATGAGAAAAATCTAACTAAAATGATAGAAATAGCTCGAGCTTTTCTTAACTATAAA
129 ATTATTAATATGAGAAAAATC-AACTAAAATGA-AGAAATAGCTCGAGCTTTTCTCAACTATAAA
*
45440 AAAAAATTAAGACTTGACATAAATGATTCAATATTAGTA
192 AAAAAATTAAGACTTGACATAAATGACTCAATATTA-TA
**
45479 AATGAGATGAGGCCAATAAGATAAATTTGAAGGCAAGTTTATCTATCATTT-TCATTGCTGAGAA
1 AATGAGATGAGGCCAATAAGATAAATTTGAAGGCAACATTATCTATCATTTGT-ATTGCTGAGAA
* * * * * * *
45543 AATATGAGAAAACAACTGAAAAAAAATGAAGGAGAGAAAAGACACTGACATATTGCCCAATAATT
65 AATATGAGAAAGCAGCTGAAAAAAAAAGAA-GAGA-AAGAGAAACTGACATATTG-CTAGTAATT
*
45608 -GTACCT-TTAATATGAGAAAAATCATACTAACAA-GAACGAAATAGCTAC-AGCTTTTCTCAAC
127 AG-A-TTATTAATATGAGAAAAATCA-ACTAA-AATGAA-GAAATAGCT-CGAGCTTTTCTCAAC
* * * * *
45669 CATAAAAAAAAACTAAGATTTTGACATAATTGACTCAAAATTATA
186 TATAAAAAAAAATTAAGA-CTTGACATAAATGACTCAATATTATA
45714 AAT
1 AAT
45717 TCAATAATTT
Statistics
Matches: 403, Mismatches: 50, Indels: 33
0.83 0.10 0.07
Matches are distributed among these distances:
230 1 0.00
231 118 0.29
232 2 0.00
233 79 0.20
234 26 0.06
235 138 0.34
236 39 0.10
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (229 bp):
AATGAGATGAGGCCAATAAGATAAATTTGAAGGCAACATTATCTATCATTTGTATTGCTGAGAAA
ATATGAGAAAGCAGCTGAAAAAAAAAGAAGAGAAAGAGAAACTGACATATTGCTAGTAATTAGAT
TATTAATATGAGAAAAATCAACTAAAATGAAGAAATAGCTCGAGCTTTTCTCAACTATAAAAAAA
AATTAAGACTTGACATAAATGACTCAATATTATA
Found at i:45759 original size:15 final size:16
Alignment explanation
Indices: 45727--45759 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45717 TCAATAATTT
*
45727 TAAAATTTTTTTACAA
1 TAAAAGTTTTTTACAA
45743 TAAAAGTTTTTTA-AA
1 TAAAAGTTTTTTACAA
45758 TA
1 TA
45760 TTTGATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
TAAAAGTTTTTTACAA
Found at i:47174 original size:14 final size:14
Alignment explanation
Indices: 47157--47196 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
47147 GGCAGCCACT
47157 GAGATGAGGCCAAC
1 GAGATGAGGCCAAC
*
47171 GAGATGAGGCCAAT
1 GAGATGAGGCCAAC
*
47185 GAGATAAGGCCA
1 GAGATGAGGCCA
47197 GATAAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.35, T:0.10
Consensus pattern (14 bp):
GAGATGAGGCCAAC
Found at i:47695 original size:230 final size:230
Alignment explanation
Indices: 47196--48065 Score: 1034
Period size: 235 Copynumber: 3.8 Consensus size: 230
47186 AGATAAGGCC
* * *
47196 AGATAAATTTGA-GATCAATCTTATCTATCATTTGTATTGTTGAAAAAATATAAAAAA-AAAT-A
1 AGATAAATTTGAGGA-CAATCTTATCTATCATTTGTATTGCTGAGAAAATATAAAAAACAACTAA
** * * *
47258 ATTAAA--AA-AAAGA-AA-ATACTGATATATTGTTAGTAATTAAACTATTAGTATGAGAAAAAT
65 AAAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAAAT
* *
47318 CCAATTAAAATGATAGAAATAGCTCAAGCTTTTCTTAACCATAAAAAAAAATCAAGACTTAACAT
130 CCAACTAAAATGATAGAAATAGCTCAAGCTTTTCTCAACCAT-AAAAAAAATCAAGACTTAACAT
* * *
47383 AAATGACTTAATATTTGCCAATGATATGAGGCCAATA
194 AAATGACTCAATATTAGCCAATGAGATGAGGCCAATA
* * * *
47420 AGATAAATTTGAGGGCAATCTTATCTATCATTTATATTTCTGAGAAAATATAAAAAAGCAGCT-A
1 AGATAAATTTGAGGACAATCTTATCTATCATTTGTATTGCTGAGAAAATATAAAAAA-CAACTAA
*
47484 AAAAAAGGAAGAAAGAGAAGACACTGACATATTACTAGTAATTAAACTATTAGTATGAGAAAAAT
65 AAAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAAAT
* *
47549 CCAACTAAAATGATAGAAATAGCTCAAGCTTTTCTCAACTATAAAAAAAATCAAGACTTAATATA
130 CCAACTAAAATGATAGAAATAGCTCAAGCTTTTCTCAACCATAAAAAAAATCAAGACTTAACATA
*
47614 AATGACTCAATATTAGCCAATGAGATGAGGCCATTA
195 AATGACTCAATATTAGCCAATGAGATGAGGCCAATA
* * * * **
47650 AGATAAATTTGAGGACAACCTTATCTATCATTTGTATTGCTGAGAAAATTTGAGAAAGCAGTTGA
1 AGATAAATTTGAGGACAATCTTATCTATCATTTGTATTGCTGAGAAAATAT-AAAAAACAACT--
*
47715 AAAAAAAAGGAAGAAAGAGAAGATACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAA
63 AAAAAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAA
** * * * *
47780 ATCTTACTAAAATGATAGAAATAGCTCGAGCTTTTCTTAACCATAAAAAAAGGATCAAAACTTAG
128 ATCCAACTAAAATGATAGAAATAGCTCAAGCTTTTCTCAACCATAAAAAAA--ATCAAGACTTAA
*
47845 CATAAATGACTCAATATTAGTCAATGAGATGAGGCCAATA
191 CATAAATGACTCAATATTAGCCAATGAGATGAGGCCAATA
* *
47885 AGATAAATTTGAAGG-CAAGT-TTATCTATCATTT-TCATTACTGAGAAAATATGAGAAAACAAC
1 AGATAAATTTG-AGGACAA-TCTTATCTATCATTTGT-ATTGCTGAGAAAATAT-AAAAAACAAC
* * * * * * * * *
47947 TGAAAAAAATGAAGGAGAGAAAAGACACTGACATATTGCCCAATAATTGTACCT-TTAATATGAG
62 TAAAAAAAAGGAA-GAAAGAGAAGACACTGACATATTG-CTAGTAATT-AAACTATTAGTATGAG
**
48011 AAAAATCGTACTAACAA-GA-ACGAAATAGCT-AGAGCTTTTCTCAACCATAAAAAAA
124 AAAAATCCAACTAA-AATGATA-GAAATAGCTCA-AGCTTTTCTCAACCATAAAAAAA
48066 GAAAAAAAAA
Statistics
Matches: 563, Mismatches: 60, Indels: 35
0.86 0.09 0.05
Matches are distributed among these distances:
224 50 0.09
225 1 0.00
226 7 0.01
228 2 0.00
229 5 0.01
230 106 0.19
231 84 0.15
233 118 0.21
234 23 0.04
235 159 0.28
236 8 0.01
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (230 bp):
AGATAAATTTGAGGACAATCTTATCTATCATTTGTATTGCTGAGAAAATATAAAAAACAACTAAA
AAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAAATC
CAACTAAAATGATAGAAATAGCTCAAGCTTTTCTCAACCATAAAAAAAATCAAGACTTAACATAA
ATGACTCAATATTAGCCAATGAGATGAGGCCAATA
Found at i:48296 original size:26 final size:25
Alignment explanation
Indices: 48260--48309 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
48250 TGTCATGAAG
48260 AATTTTTAATTGAATTATT-TTTAA
1 AATTTTTAATTGAATTATTATTTAA
*
48284 AATTTTATCAATTGATTTATTATTTA
1 AATTTT-T-AATTGAATTATTATTTA
48310 TATGAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 1 0.05
26 11 0.50
27 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (25 bp):
AATTTTTAATTGAATTATTATTTAA
Found at i:49555 original size:14 final size:14
Alignment explanation
Indices: 49536--49575 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
49526 CTAGCCCACT
49536 GAGATGAGGCCAAC
1 GAGATGAGGCCAAC
*
49550 GAGATGAGGCCAAT
1 GAGATGAGGCCAAC
49564 GAGATGAGGCCA
1 GAGATGAGGCCA
49576 GATAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.38, T:0.10
Consensus pattern (14 bp):
GAGATGAGGCCAAC
Found at i:50469 original size:236 final size:232
Alignment explanation
Indices: 49558--50675 Score: 1310
Period size: 236 Copynumber: 4.9 Consensus size: 232
49548 ACGAGATGAG
* * *
49558 GCCAATGAGATGAGGCC----AGATAAATTTGA-GATCAATCTTATCTATTATTTGTATTGTTGA
1 GCCAATGAGATGAGGCCAATAAGATAAATTTGAGGA-CAACCTTATCTATCATTTGTATTGCTGA
** * * *
49618 GAAAATAT-A-AAA--AAAT-AATTAAAA--AA-AAAGA-AA-ACATTGACATATTGCTAATAAT
65 GAAAATATGAGAAAGCAGCTGAA-AAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGTAAT
* * * * * * *
49673 TTAACTATTAATATGAGAAAAATTCAATTAAAATGATAGAAATAGTTCGAGCTTTTCTTAATCAT
129 TAAACTATTAGTATGAGAAAAATCCAACTAAAATGATAGAAATAGCTCGAGCTTTTCTCAACCAT
49738 -AAAAAAAATCAAGACTTGACATAAATGACTCAATATTA
194 AAAAAAAAATCAAGACTTGACATAAATGACTCAATATTA
* * ** * **
49776 GCCAATGAGATGAGGCGAATAAGATAAATTTAAAAACAATCTTATCTATCATTTGTATTATTGAG
1 GCCAATGAGATGAGGCCAATAAGATAAATTTGAGGACAACCTTATCTATCATTTGTATTGCTGAG
* *
49841 AAAATATGATAAAGTAGCT-AAAAAAA--AAGAAAGAGAAGACACTGACATATTGCTAGTAATTA
66 AAAATATGAGAAAGCAGCTGAAAAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTA
*
49903 AACTATTAGTATGAGAAAAATCCAACTAAAATGATAGAAATAGCTCGAGCTTTTCTCAACAATAA
131 AACTATTAGTATGAGAAAAATCCAACTAAAATGATAGAAATAGCTCGAGCTTTTCTCAACCAT-A
49968 AAAAAAAATCAAGACTTGACATAAATGACTCAATATTA
195 AAAAAAAATCAAGACTTGACATAAATGACTCAATATTA
* *
50006 GCCAATGAGACGAGGCCAATAAGATAAATTTGAGGGCAACCTTATCTATCATTTGTATTGCTGAG
1 GCCAATGAGATGAGGCCAATAAGATAAATTTGAGGACAACCTTATCTATCATTTGTATTGCTGAG
*
50071 AAAATATGAGAAAGCAGCTGAAAAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGCAATTA
66 AAAATATGAGAAAGCAGCTGAAAAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTA
* *
50136 AACTATTACTATGAGAAAAATCCAACTAAAATGATAGAAATAGCTCGAGCTTTTCTCAACTATAA
131 AACTATTAGTATGAGAAAAATCCAACTAAAATGATAGAAATAGCTCGAGCTTTTCTCAACCATAA
*
50201 AAAAAAATCAAGACTTGATATAAATGACTCAATATTA
196 AAAAAAATCAAGACTTGACATAAATGACTCAATATTA
* * * *
50238 GCCAATGAGATGAGGTCAATAAGATAAATTTGAGGACAACCTTATTTATTATTTGTATTGCTGAT
1 GCCAATGAGATGAGGCCAATAAGATAAATTTGAGGACAACCTTATCTATCATTTGTATTGCTGAG
* * * *
50303 AAATTTTGAGAAAGCAGCTGAAAAAAAAAACGGAAGAAAGAGAAGATACTGACATATTTCTAGTA
66 AAAATATGAGAAAGCAGCTG---AAAAAAA-GGAAGAAAGAGAAGACACTGACATATTGCTAGTA
* ** *
50368 ATTAAACTATTTGTATGAGAAAAATCTTACTAAAATGATAGAAATAGCTCGAGCTTTTCTTAACC
127 ATTAAACTATTAGTATGAGAAAAATCCAACTAAAATGATAGAAATAGCTCGAGCTTTTCTCAACC
* * *
50433 ATAAAAAAAAATCAAAACTTGGCATAAATAACTCAATATTA
192 ATAAAAAAAAATCAAGACTTGACATAAATGACTCAATATTA
* * ** ** * *
50474 GCCAATGAGATGAGGCCAATATGGTAAATTTGAAGG-CAAATTTATCTATCATTTACATTACTAA
1 GCCAATGAGATGAGGCCAATAAGATAAATTTG-AGGACAACCTTATCTATCATTTGTATTGCTGA
* * * ** * * * *
50538 GAAAATATAAAAAAACAATTGAAAAAAA-TAGAGAAGAGAGAAGATACTGACATATTGCCCAATA
65 GAAAATATGAGAAAGCAGCTGAAAAAAAGGA-AGAA-AGAGAAGACACTGACATATTG-CTAGTA
** * * * * * * *
50602 ATTGTACTATTAATAAGGGAAAAAT-CATAATAATAA-GAAAGAAATAGTTAGAGCTTTTCTCAA
127 ATTAAACTATTAGTATGAGAAAAATCCA-ACTAA-AATGATAGAAATAGCTCGAGCTTTTCTCAA
50665 CCATAAAAAAA
190 CCATAAAAAAA
50676 GAAAAAAAAA
Statistics
Matches: 783, Mismatches: 90, Indels: 38
0.86 0.10 0.04
Matches are distributed among these distances:
218 16 0.02
222 45 0.06
223 2 0.00
224 3 0.00
225 6 0.01
226 9 0.01
227 2 0.00
228 77 0.10
230 111 0.14
231 8 0.01
232 119 0.15
233 123 0.16
234 61 0.08
235 9 0.01
236 189 0.24
237 3 0.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.27
Consensus pattern (232 bp):
GCCAATGAGATGAGGCCAATAAGATAAATTTGAGGACAACCTTATCTATCATTTGTATTGCTGAG
AAAATATGAGAAAGCAGCTGAAAAAAAGGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTA
AACTATTAGTATGAGAAAAATCCAACTAAAATGATAGAAATAGCTCGAGCTTTTCTCAACCATAA
AAAAAAATCAAGACTTGACATAAATGACTCAATATTA
Found at i:52919 original size:233 final size:229
Alignment explanation
Indices: 52185--53285 Score: 1348
Period size: 229 Copynumber: 4.8 Consensus size: 229
52175 AGATAAGGCC
* ** * ** * *
52185 AGATAAATTTGAGATCAATATTATCTATCATTTGTATTGTTGAGAAAATATAAAAAAGTAATT--
1 AGATAAATTTGAG-GCAACCTTATCTATCATTTATATTACTGAGAAAATATGAAAAAGCAATTAA
* *
52248 AAAAA--AA-AAAGA-AA-ACACTGACATATTGCTAGTAATTAAATTATTAGTATGAGAAAAATC
65 AAAAAGGAAGAAAGAGAAGATACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAAATC
* * *
52308 TAATTAAAATGATAGAAATAGCTTGAGCTTTTTTTAACCATAAAAAAAAATCAAGACTTGACATA
130 TAACTAAAATGATAGAAATAGC-TGAGCTTTTCTCAACCATAAAAAAAAATCAAGACTTGACATA
* * * * *
52373 AATGACTCAATATTTGTCAATGACATGAGGCCAACA
194 AATGACTCAATATTAGCCAATAAGATGAGGCCAATA
* * *
52409 AGATAAATTTGAAGGCAATCTTATCTATCATTTATATTTA-TGAGAAAATATGAAAAAAC-ACT-
1 AGATAAATTTG-AGGCAACCTTATCTATCATTTATA-TTACTGAGAAAATATGAAAAAGCAATTA
52471 AAAAAAGGAAGAAAGAGAAGATACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAAAT
64 AAAAAAGGAAGAAAGAGAAGATACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAAAT
* * *
52536 CTAACTAAAATGATAGAAATAGCTCGAGCTTATCTCAACAATAAAAAAAAATTAAGACTTGACAT
129 CTAACTAAAATGATAGAAATAGCT-GAGCTTTTCTCAACCATAAAAAAAAATCAAGACTTGACAT
52601 AAATGACTCAATATTAGCCAATAAGATGAGGCCAATA
193 AAATGACTCAATATTAGCCAATAAGATGAGGCCAATA
*
52638 AGATAAATTTGAGGGCAACCTTATCTATCATTTATATTACTGAGAAAATATGAGAAAGCAATTGA
1 AGATAAATTTGA-GGCAACCTTATCTATCATTTATATTACTGAGAAAATATGAAAAAGCAATT-A
* * * *
52703 AAAAAAGGAAGAAAGAGAAGACACTGACATATTGTTAGCAATTAAACTATTACTATGAGAAAAAT
64 AAAAAAGGAAGAAAGAGAAGATACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAAAT
* * *
52768 CCAACTAAAATGATAGAAATAGCTGAAGCTTTTCTCAACTATAAAAAAAAAATCAAGACTTGATA
129 CTAACTAAAATGATAGAAATAGCTG-AGCTTTTCTCAACCAT-AAAAAAAAATCAAGACTTGACA
*
52833 TAAATGACTCAATATTAGCCAATGAGATGAGGCCAATA
192 TAAATGACTCAATATTAGCCAATAAGATGAGGCCAATA
* * *
52871 AGATAAATTTGAGGACAACCTTATCTATCATTTGTATTGCTGAGAAAATTTGAGAAAGCAGCTGA
1 AGATAAATTTGAGG-CAACCTTATCTATCATTTATATTACTGAGAAAATATGA-AAA--AGC--A
* * * *
52936 A-AAAAAAAATGAAGAAAAAGAAGATACTGACATATTGCTAGTAATTAAACTATTAGTATGAAAA
60 ATTAAAAAAAGGAAGAAAGAGAAGATACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAA
* * * *
53000 AAATCTTACTAAAATGATAAAAATAGCTCGAGCTTTTCTTAACCATAAAAAAAAATCAAAACTTG
125 AAATCTAACTAAAATGATAGAAATAGCT-GAGCTTTTCTCAACCATAAAAAAAAATCAAGACTTG
* *
53065 GCATAAATGACTCAATATTAGCCAATAAGATGAGGCGAATA
189 ACATAAATGACTCAATATTAGCCAATAAGATGAGGCCAATA
* ** * *
53106 TGATAAATTTGAAGGCAAATTTATCTATCATTT-TCATTACTAAGAAAATATGAAAAAACAATTA
1 AGATAAATTTG-AGGCAACCTTATCTATCATTTAT-ATTACTGAGAAAATATGAAAAAGCAATTA
* * * * * * * *
53170 AAAAAATAGAGGAGAGAGAAGATACTGACATATTGCCCAATAATTATACTATTAATAAGAGAAAA
64 AAAAAA-GGAAGAAAGAGAAGATACTGACATATTG-CTAGTAATTAAACTATTAGTATGAGAAAA
* *
53235 ATC-ATACTGATAA-GAAAGAAATAGCTAGAGCTTTTCTCAACCATAAAAAAA
127 ATCTA-ACT-AAAATGATAGAAATAGCT-GAGCTTTTCTCAACCATAAAAAAA
53286 GAAAAAAAAC
Statistics
Matches: 766, Mismatches: 81, Indels: 51
0.85 0.09 0.06
Matches are distributed among these distances:
223 2 0.00
224 51 0.07
225 4 0.01
226 2 0.00
227 5 0.01
228 7 0.01
229 182 0.24
230 4 0.01
231 8 0.01
232 126 0.16
233 167 0.22
234 9 0.01
235 96 0.13
236 100 0.13
237 1 0.00
238 2 0.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (229 bp):
AGATAAATTTGAGGCAACCTTATCTATCATTTATATTACTGAGAAAATATGAAAAAGCAATTAAA
AAAAGGAAGAAAGAGAAGATACTGACATATTGCTAGTAATTAAACTATTAGTATGAGAAAAATCT
AACTAAAATGATAGAAATAGCTGAGCTTTTCTCAACCATAAAAAAAAATCAAGACTTGACATAAA
TGACTCAATATTAGCCAATAAGATGAGGCCAATA
Found at i:53050 original size:468 final size:459
Alignment explanation
Indices: 52185--53285 Score: 1425
Period size: 468 Copynumber: 2.4 Consensus size: 459
52175 AGATAAGGCC
** * ** * *
52185 AGATAAATTTGAGATCAATATTATCTATCATTTGTATTGTTGAGAAAATATAAAAAAGTAATT--
1 AGATAAATTTGAGGGCAAAATTATCTATCATTT-TATTACTGAGAAAATATGAAAAAGCAATTAA
* * *
52248 AAAAA-AA-AAAGA-AA-ACACTGACATATTGCTAGTAATTAAATTATTAGTATGAGAAAAATCT
65 AAAAAGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTAAACTATTAATATGAGAAAAATCC
* * *
52309 AATTAAAATGATAGAAATAGCTTG-AGCTTTTTTTAACCAT-AAAAAAAAATCAAGACTTGACAT
130 AACTAAAATGATAGAAATAGC-TGAAGCTTTTCTCAACCATAAAAAAAAAATCAAGACTTGACAT
* * *
52372 AAATGACTCAATATTTGTCAATGACATGAGGCCAACAAGATAAATTTGAAGGCAATCTTATCTAT
194 AAATGACTCAATATTAGCCAATGACATGAGGCCAACAAGATAAATTTGAAGGCAACCTTATCTAT
* *
52437 CATTTATATTTATGAGAAAATATGAAAAAACACTAAAAAAGGAAGAAAGAGAAGATACTGACATA
259 CATTTATATTGATGAGAAAATATGAAAAAACACTAAAAAAGGAAGAAAAAGAAGATACTGACATA
* *
52502 TTGCTAGTAATTAAACTATTAGTATGAGAAAAATCTAACTAAAATGATAGAAATAGCTCGAGCTT
324 TTGCTAGTAATTAAACTATTAGTATGAAAAAAATCTAACTAAAATGATAAAAATAGCTCGAGCTT
* *
52567 ATCTCAACAATAAAAAAAAATTAAGACTTGACATAAATGACTCAATATTAGCCAATAAGATGAGG
389 ATCTCAACAATAAAAAAAAATCAAAACTTGACATAAATGACTCAATATTAGCCAATAAGATGAGG
52632 CCAATA
454 CCAATA
** *
52638 AGATAAATTTGAGGGCAACCTTATCTATCATTTATATTACTGAGAAAATATGAGAAAGCAATTGA
1 AGATAAATTTGAGGGCAAAATTATCTATCATTT-TATTACTGAGAAAATATGAAAAAGCAATT-A
* * *
52703 AAAAAAGGAAGAAAGAGAAGACACTGACATATTGTTAGCAATTAAACTATTACTATGAGAAAAAT
64 AAAAAA-GAAGAAAGAGAAGACACTGACATATTGCTAGTAATTAAACTATTAATATGAGAAAAAT
* *
52768 CCAACTAAAATGATAGAAATAGCTGAAGCTTTTCTCAACTATAAAAAAAAAATCAAGACTTGATA
128 CCAACTAAAATGATAGAAATAGCTGAAGCTTTTCTCAACCATAAAAAAAAAATCAAGACTTGACA
* *
52833 TAAATGACTCAATATTAGCCAATGAGATGAGGCCAATAAGATAAATTTG-AGGACAACCTTATCT
193 TAAATGACTCAATATTAGCCAATGACATGAGGCCAACAAGATAAATTTGAAGG-CAACCTTATCT
* * * * * *
52897 ATCATTTGTATTGCTGAGAAAATTTGAGAAAGCAGCTGAAAAAAAAAATGAAGAAAAAGAAGATA
257 ATCATTTATATTGATGAGAAAATATGAAAAAACA-CT-----AAAAAAGGAAGAAAAAGAAGATA
*
52962 CTGACATATTGCTAGTAATTAAACTATTAGTATGAAAAAAATCTTACTAAAATGATAAAAATAGC
316 CTGACATATTGCTAGTAATTAAACTATTAGTATGAAAAAAATCTAACTAAAATGATAAAAATAGC
* * * *
53027 TCGAGCTTTTCTTAACCATAAAAAAAAATCAAAACTTGGCATAAATGACTCAATATTAGCCAATA
381 TCGAGCTTATCTCAACAATAAAAAAAAATCAAAACTTGACATAAATGACTCAATATTAGCCAATA
*
53092 AGATGAGGCGAATA
446 AGATGAGGCCAATA
* * * * *
53106 TGATAAATTTGAAGGCAAATTTATCTATCATTTTCATTACTAAGAAAATATGAAAAAACAATTAA
1 AGATAAATTTGAGGGCAAAATTATCTATCATTTT-ATTACTGAGAAAATATGAAAAAGCAATT-A
* * * * * * *
53171 AAAAATAGAGGAGAGAGAAGATACTGACATATTGCCCAATAATTATACTATTAATAAGAGAAAAA
64 AAAAA-AGAAGAAAGAGAAGACACTGACATATTG-CTAGTAATTAAACTATTAATATGAGAAAAA
* *
53236 T-CATACTGATAA-GAAAGAAATAGCT-AGAGCTTTTCTCAACCATAAAAAAA
127 TCCA-ACT-AAAATGATAGAAATAGCTGA-AGCTTTTCTCAACCATAAAAAAA
53286 GAAAAAAAAC
Statistics
Matches: 561, Mismatches: 64, Indels: 30
0.86 0.10 0.05
Matches are distributed among these distances:
453 53 0.09
456 5 0.01
458 2 0.00
459 5 0.01
460 4 0.01
461 78 0.14
462 104 0.19
463 2 0.00
467 1 0.00
468 242 0.43
469 62 0.11
470 3 0.01
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (459 bp):
AGATAAATTTGAGGGCAAAATTATCTATCATTTTATTACTGAGAAAATATGAAAAAGCAATTAAA
AAAAGAAGAAAGAGAAGACACTGACATATTGCTAGTAATTAAACTATTAATATGAGAAAAATCCA
ACTAAAATGATAGAAATAGCTGAAGCTTTTCTCAACCATAAAAAAAAAATCAAGACTTGACATAA
ATGACTCAATATTAGCCAATGACATGAGGCCAACAAGATAAATTTGAAGGCAACCTTATCTATCA
TTTATATTGATGAGAAAATATGAAAAAACACTAAAAAAGGAAGAAAAAGAAGATACTGACATATT
GCTAGTAATTAAACTATTAGTATGAAAAAAATCTAACTAAAATGATAAAAATAGCTCGAGCTTAT
CTCAACAATAAAAAAAAATCAAAACTTGACATAAATGACTCAATATTAGCCAATAAGATGAGGCC
AATA
Found at i:54957 original size:27 final size:27
Alignment explanation
Indices: 54927--54981 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
54917 ATCATTTTTT
*
54927 ATAAAAATAAAATAACCACCATATTTA
1 ATAAAAACAAAATAACCACCATATTTA
*
54954 ATAAATACAAAATAACCACCATATTTA
1 ATAAAAACAAAATAACCACCATATTTA
54981 A
1 A
54982 GACAAGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.25
Consensus pattern (27 bp):
ATAAAAACAAAATAACCACCATATTTA
Found at i:57495 original size:15 final size:15
Alignment explanation
Indices: 57475--57508 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
57465 ATTTCATATT
*
57475 ATTTATTTTTATTAA
1 ATTTATTTTAATTAA
*
57490 ATTTATTTTAATTTA
1 ATTTATTTTAATTAA
57505 ATTT
1 ATTT
57509 GTTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTATTTTAATTAA
Found at i:58780 original size:15 final size:14
Alignment explanation
Indices: 58754--58794 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
58744 TTTAATTTAA
58754 AATATAATATAATT
1 AATATAATATAATT
58768 AATATAGATATAATT
1 AATATA-ATATAATT
58783 -ATGATAATATAA
1 AAT-ATAATATAA
58795 ATCAAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (14 bp):
AATATAATATAATT
Found at i:59006 original size:19 final size:19
Alignment explanation
Indices: 58973--59010 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
58963 TTTTATTTGT
*
58973 ATTTAGTTTATATTTTAAAA
1 ATTTAGTTTA-AATTTAAAA
58993 ATTTA-TTTAAATTTAAAA
1 ATTTAGTTTAAATTTAAAA
59011 TTATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTAGTTTAAATTTAAAA
Found at i:59045 original size:20 final size:21
Alignment explanation
Indices: 59022--59061 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59012 TATAAAAAAT
59022 ATAATT-AAATATATTTATAC
1 ATAATTAAAATATATTTATAC
*
59042 ATAATTAAAATTTATTTATA
1 ATAATTAAAATATATTTATA
59062 AATTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATTAAAATATATTTATAC
Found at i:59069 original size:21 final size:21
Alignment explanation
Indices: 59022--59069 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
59012 TATAAAAAAT
*
59022 ATAATT-AAATATATTTATAC
1 ATAATTAAAATATATTTATAA
*
59042 ATAATTAAAATTTATTTATAA
1 ATAATTAAAATATATTTATAA
*
59063 ATTATTA
1 ATAATTA
59070 TTATATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATTAAAATATATTTATAA
Done.